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- PDB-5yhm: Crystal structure of dehydroquinate dehydratase with tris induced... -

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Basic information

Entry
Database: PDB / ID: 5yhm
TitleCrystal structure of dehydroquinate dehydratase with tris induced oligomerisation at 1.907 Angstrom resolution
Components(3-dehydroquinate dehydratase) x 2
KeywordsLYASE
Function / homology
Function and homology information


quinate catabolic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
Dehydroquinase, class II / Dehydroquinase, class II, conserved site / Dehydroquinase class II signature. / Dehydroquinase, class II / Dehydroquinase, class II superfamily / Dehydroquinase class II / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsIqbal, N. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of dehydroquinate dehydratase with tris induced oligomerisation at 1.907 Angstrom resolution
Authors: Iqbal, N. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionSep 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
C: 3-dehydroquinate dehydratase
D: 3-dehydroquinate dehydratase
E: 3-dehydroquinate dehydratase
F: 3-dehydroquinate dehydratase
G: 3-dehydroquinate dehydratase
H: 3-dehydroquinate dehydratase
I: 3-dehydroquinate dehydratase
J: 3-dehydroquinate dehydratase
K: 3-dehydroquinate dehydratase
L: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,49328
Polymers190,85212
Non-polymers1,64116
Water9,116506
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31120 Å2
ΔGint-316 kcal/mol
Surface area63830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.904, 155.606, 155.912
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
3-dehydroquinate dehydratase / 3-dehydroquinase


Mass: 15886.130 Da / Num. of mol.: 11 / Fragment: UNP residues 3-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria)
Strain: ATCC 17978 / NCDC KC 755 / Gene: aroQ, A1S_2009 / Production host: Escherichia coli (E. coli) / References: UniProt: A3M692
#2: Protein 3-dehydroquinate dehydratase / 3-dehydroquinase


Mass: 16104.404 Da / Num. of mol.: 1 / Fragment: UNP residues 1-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377) (bacteria)
Strain: ATCC 17978 / NCDC KC 755 / Gene: aroQ, A1S_2009 / Production host: Escherichia coli (E. coli) / References: UniProt: A3M692
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.5M Ammonium sulphate, 0.1M tris, 12% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.91→45.7 Å / Num. obs: 139447 / % possible obs: 89.8 % / Redundancy: 3.2 % / Rpim(I) all: 0.134 / Net I/σ(I): 5.96
Reflection shellResolution: 1.91→1.956 Å / Num. unique obs: 1715

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata processing
Cootmodel building
MOLREPphasing
XDSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B6P

5b6p


Resolution: 1.91→45.7 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.976 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.157 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24779 1465 1.1 %RANDOM
Rwork0.19992 ---
obs0.20044 137982 89.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.754 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å2-0 Å2
2---0.71 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.91→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13466 0 92 506 14064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01913806
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213541
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.95318786
X-RAY DIFFRACTIONr_angle_other_deg1.048330971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4851730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59524.314612
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.447152272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9241572
X-RAY DIFFRACTIONr_chiral_restr0.1010.22226
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215626
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023182
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7024.3336960
X-RAY DIFFRACTIONr_mcbond_other3.7014.3336955
X-RAY DIFFRACTIONr_mcangle_it5.7696.4748674
X-RAY DIFFRACTIONr_mcangle_other5.7696.4758675
X-RAY DIFFRACTIONr_scbond_it4.1124.8466846
X-RAY DIFFRACTIONr_scbond_other4.1114.8466846
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.437.10210113
X-RAY DIFFRACTIONr_long_range_B_refined10.35640.69857335
X-RAY DIFFRACTIONr_long_range_B_other10.35340.67657143
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.907→1.956 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 74 -
Rwork0.4 7026 -
obs--62.43 %

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